Contacts of the strand formed by residues 218 - 227 (chain A) in PDB entry 3KYS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A GLN* 3.2 29.2 + - - -
214A ARG* 2.7 47.1 + - - -
215A ASP* 2.9 25.9 + - - +
216A PRO 3.4 1.0 + - - -
217A ASP* 1.3 79.3 + - - +
219A TYR* 1.3 60.7 + - - +
220C ASN* 6.0 3.4 - - - +
221C LYS 3.5 3.1 - - - -
222C HIS* 4.1 5.6 + - - +
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Residues in contact with TYR 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A GLU* 2.6 49.4 + - + +
212A GLN 3.5 5.4 - - - -
213A GLN* 3.6 19.7 - - - +
218A SER* 1.3 75.3 - - - +
220A ASN* 1.3 65.0 + - - +
221A LYS* 3.5 20.6 + - + +
219C TYR* 3.7 35.9 - + - -
220C ASN* 2.9 8.4 + - - +
221C LYS* 2.7 48.5 + - + +
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Residues in contact with ASN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A LEU* 4.5 2.0 + - - +
211A GLU* 3.2 4.7 - - - +
212A GLN* 2.7 55.1 + - + +
219A TYR* 1.3 80.9 - - - +
221A LYS* 1.3 73.0 + - - +
222A HIS* 4.1 9.5 - - - +
281A CYS* 6.2 0.4 - - - +
282A ASN 5.8 0.4 + - - -
284A GLN* 4.1 19.9 - - - +
218C SER* 5.8 1.6 - - - -
219C TYR 3.4 14.7 + - - +
220C ASN* 3.6 12.8 - - - +
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Residues in contact with LYS 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 5.5 1.0 + - - -
209A PHE* 3.5 47.1 - - + -
210A LEU 3.4 7.4 - - - +
211A GLU* 4.3 5.6 + - + +
219A TYR* 3.5 28.8 + - + +
220A ASN* 1.3 79.4 + - - +
222A HIS* 1.3 64.9 + - - +
223A LEU* 4.2 12.9 - - + +
294A THR* 5.7 1.2 + - - -
340A ARG* 5.5 1.2 - - - +
217C ASP 3.5 4.0 - - - +
218C SER* 3.6 1.2 - - - -
219C TYR* 3.0 43.2 + - + +
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Residues in contact with HIS 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A PHE* 3.0 5.7 - - - +
210A LEU* 2.8 47.0 + - + +
220A ASN* 4.5 9.0 - - - +
221A LYS* 1.3 75.4 - - - +
223A LEU* 1.3 72.1 + - - +
224A PHE* 3.8 21.9 - + - -
278A ASP* 2.8 53.3 + - - -
280A ASN 3.6 16.1 + - - -
281A CYS* 3.3 28.7 - - + +
214C ARG* 5.0 0.4 + - - -
217C ASP* 3.2 12.0 + - + -
218C SER* 4.2 9.1 + - - +
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A SER* 3.6 20.4 - - - +
208A ALA 3.6 2.7 - - - +
209A PHE* 3.7 17.3 - - + -
221A LYS* 4.2 17.0 - - + +
222A HIS* 1.3 90.7 + - - +
224A PHE* 1.3 61.4 + - - +
225A VAL 4.4 6.5 - - - +
226A HIS* 4.2 8.5 - - + -
229A HIS* 4.0 29.8 - - + +
278A ASP* 3.6 1.6 - - - +
216C PRO 3.7 19.1 - - - +
217C ASP* 2.9 38.9 + - - +
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Residues in contact with PHE 224 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208A ALA* 2.8 26.1 + - + +
209A PHE* 3.6 28.3 - - - -
210A LEU* 3.7 21.5 - - + -
222A HIS* 3.8 12.8 - + - -
223A LEU* 1.3 73.3 - - - +
225A VAL* 1.3 63.3 + - - +
277A ALA* 3.4 0.7 - - - -
278A ASP* 2.7 44.1 + - - +
279A LEU* 3.9 13.2 - - + -
281A CYS* 4.1 12.3 - - - -
291A TYR* 4.2 12.8 - + - -
343A MET* 4.9 3.4 - - - -
344A P1L 3.9 22.4 - - + -
351A ILE* 4.0 35.0 - - + -
401A ALA* 3.4 6.8 - - - +
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE* 3.8 28.3 - - + -
207A SER* 3.6 2.1 + - - -
208A ALA* 3.3 26.5 + - + +
223A LEU* 4.4 1.0 - - - +
224A PHE* 1.3 82.4 + - - +
226A HIS* 1.3 67.5 + - - +
275A PHE* 3.6 34.5 - - + -
276A TRP 4.7 1.3 - - - +
277A ALA* 3.8 23.8 - - + -
344A P1L 4.0 24.5 - - + -
392A PHE* 4.5 1.3 - - + -
401A ALA* 4.2 7.0 - - - -
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Residues in contact with HIS 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A PHE 3.4 7.0 - - - +
207A SER* 4.7 0.9 - - - +
223A LEU* 4.2 10.3 - - + -
225A VAL* 1.3 82.0 - - - +
227A ILE* 1.3 60.4 + - - +
228A GLY 5.6 0.2 + - - -
229A HIS* 3.2 50.0 + - + +
275A PHE* 4.8 1.6 - - - -
401A ALA* 3.7 26.5 + - + +
403A HIS* 3.3 25.3 + + - +
216C PRO* 4.6 16.1 - - + +
217C ASP* 2.9 31.1 + - - -
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Residues in contact with ILE 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A ILE* 5.2 4.0 - - + -
203A LEU* 3.9 20.9 - - + +
204A VAL 5.1 0.9 - - - +
205A GLU* 3.5 3.3 - - - -
206A PHE* 2.9 48.9 + - + +
226A HIS* 1.3 77.0 - - - +
228A GLY* 1.3 66.5 + - - +
229A HIS* 3.6 6.8 - - - -
273A VAL* 4.5 8.3 - - + -
275A PHE* 3.5 32.1 - - + -
388A MET* 4.4 16.8 - - + -
403A HIS* 3.7 29.6 - - + +
405A ILE* 4.5 12.1 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il